BioC 3.3: CHECK report for flowCore on linux2.bioconductor.org

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings flowCore_1.37.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/flowCore.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘flowCore/DESCRIPTION’ ... OK
* this is package ‘flowCore’ version ‘1.37.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
  src/boost_regex/c_regex_traits.o src/boost_regex/cpp_regex_traits.o
  src/boost_regex/cregex.o src/boost_regex/fileiter.o
  src/boost_regex/icu.o src/boost_regex/instances.o
  src/boost_regex/posix_api.o src/boost_regex/regex.o
  src/boost_regex/regex_debug.o src/boost_regex/regex_raw_buffer.o
  src/boost_regex/regex_traits_defaults.o
  src/boost_regex/static_mutex.o src/boost_regex/usinstances.o
  src/boost_regex/w32_regex_traits.o src/boost_regex/wc_regex_traits.o
  src/boost_regex/wide_posix_api.o src/boost_regex/winstances.o
Object files/libraries should not be included in a source package.
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘flowCore’ can be installed ... [66s/66s] OK
* checking installed package size ... NOTE
  installed size is 32.1Mb
  sub-directories of 1Mb or more:
    data      5.0Mb
    doc       1.3Mb
    extdata   1.1Mb
    lib      19.6Mb
    libs      3.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘Rgraphviz’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
rbind2,flowSet-flowSet: warning in assign(i, x[[i]], env = env):
  partial argument match of 'env' to 'envir'
rbind2,flowSet-flowSet: warning in assign(i, y[[i]], env = env):
  partial argument match of 'env' to 'envir'
%in%,flowFrame-norm2Filter: no visible global function definition for
  ‘cov.rob’
spillover,flowSet : <anonymous>: no visible global function definition
  for ‘rangeGate’
split,flowFrame-factor: no visible binding for global variable ‘i’
summary,workFlow: no visible binding for global variable ‘wf’
Undefined global functions or variables:
  cov.rob i rangeGate wf
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [24s/24s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run-all.R’ [6s/6s]
 [6s/6s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/flowCore.Rcheck/00check.log’
for details.

* installing *source* package ‘flowCore’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c FastLogicle.cpp -o FastLogicle.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c Hyperlog.cpp -o Hyperlog.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c Logicle.cpp -o Logicle.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c biexponential.c -o biexponential.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c fcsTextParse.cpp -o fcsTextParse.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c hyperlogTransform.cpp -o hyperlogTransform.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c inPolygon.c -o inPolygon.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c inPolytope.c -o inPolytope.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c init.c -o init.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c logicleTransform.cpp -o logicleTransform.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c pairVectorRcppWrap.cpp -o pairVectorRcppWrap.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c uint2double.cpp -o uint2double.o
gcc -std=gnu99 -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c zeroin.c -o zeroin.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c boost_regex/c_regex_traits.cpp -o boost_regex/c_regex_traits.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c boost_regex/cpp_regex_traits.cpp -o boost_regex/cpp_regex_traits.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c boost_regex/cregex.cpp -o boost_regex/cregex.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c boost_regex/fileiter.cpp -o boost_regex/fileiter.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c boost_regex/icu.cpp -o boost_regex/icu.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c boost_regex/instances.cpp -o boost_regex/instances.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c boost_regex/regex.cpp -o boost_regex/regex.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c boost_regex/regex_raw_buffer.cpp -o boost_regex/regex_raw_buffer.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c boost_regex/regex_traits_defaults.cpp -o boost_regex/regex_traits_defaults.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c boost_regex/usinstances.cpp -o boost_regex/usinstances.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c boost_regex/w32_regex_traits.cpp -o boost_regex/w32_regex_traits.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c boost_regex/wc_regex_traits.cpp -o boost_regex/wc_regex_traits.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -c boost_regex/winstances.cpp -o boost_regex/winstances.o
mkdir -p "/home/biocbuild/bbs-3.3-bioc/meat/flowCore.Rcheck/flowCore/lib"
ar rs "/home/biocbuild/bbs-3.3-bioc/meat/flowCore.Rcheck/flowCore/lib/libboost_regex.a" boost_regex/c_regex_traits.o boost_regex/cpp_regex_traits.o boost_regex/cregex.o boost_regex/fileiter.o boost_regex/icu.o boost_regex/instances.o boost_regex/posix_api.o boost_regex/regex.o boost_regex/regex_debug.o boost_regex/regex_raw_buffer.o boost_regex/regex_traits_defaults.o boost_regex/static_mutex.o boost_regex/usinstances.o boost_regex/w32_regex_traits.o boost_regex/wc_regex_traits.o boost_regex/wide_posix_api.o boost_regex/winstances.o
ar: creating /home/biocbuild/bbs-3.3-bioc/meat/flowCore.Rcheck/flowCore/lib/libboost_regex.a
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o flowCore.so FastLogicle.o Hyperlog.o Logicle.o RcppExports.o biexponential.o fcsTextParse.o hyperlogTransform.o inPolygon.o inPolytope.o init.o logicleTransform.o pairVectorRcppWrap.o uint2double.o zeroin.o /home/biocbuild/bbs-3.3-bioc/meat/flowCore.Rcheck/flowCore/lib/libboost_regex.a -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-bioc/meat/flowCore.Rcheck/flowCore/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (flowCore)

name	user	system	elapsed
EHtrans-class	0.035	0.004	0.039
FCSTransTransform	0.869	0.020	0.889
Subset-methods	0.241	0.004	0.246
actionItem-class	0.001	0.000	0.002
arcsinhTransform	0.027	0.000	0.027
asinht-class	0.024	0.000	0.024
asinhtGml2-class	0.041	0.000	0.041
biexponentialTransform	3.463	0.044	3.510
boundaryFilter-class	0.064	0.000	0.064
characterOrTransformation-class	0.001	0.000	0.001
coerce	0.134	0.000	0.134
compensateActionItem-class	0.001	0.000	0.001
compensateView-class	0.001	0.000	0.001
compensatedParameter-class	0.109	0.000	0.109
compensation-class	0.256	0.004	0.260
dg1polynomial-class	0.022	0.000	0.022
each_col-methods	0.03	0.00	0.03
ellipsoidGate	0.047	0.000	0.048
exponential-class	0.021	0.000	0.021
expressionFilter-class	0.046	0.000	0.046
fcReference-class	0.001	0.000	0.001
filter-methods	0.568	0.015	0.584
filter-on-methods	0.074	0.000	0.074
filterList-class	0.005	0.000	0.005
filterResult-class	0.000	0.000	0.001
filterResultList-class	0.001	0.000	0.000
filterSummary-class	0.001	0.000	0.001
filterSummaryList-class	0.000	0.000	0.001
flowFrame-class	2.387	0.032	2.420
flowSet-class	2.725	0.004	2.730
fsApply	0.137	0.000	0.137
gateActionItem-class	0.001	0.000	0.001
gateView-class	0	0	0
getIndexSort-methods	0.017	0.000	0.019
hyperlog-class	1.534	0.000	1.534
hyperlogtGml2-class	0.041	0.000	0.041
identifier-methods	0.018	0.000	0.018
inverseLogicleTransform	0.573	0.004	0.577
invsplitscale-class	0.023	0.000	0.023
keyword-methods	0.667	0.004	0.671
kmeansFilter	0.169	0.000	0.169
linearTransform	0.04	0.00	0.04
lintGml2-class	0.067	0.000	0.067
lnTransform	1.109	0.000	1.109
logTransform	0.025	0.004	0.029
logarithm-class	0.024	0.000	0.024
logicalFilterResult-class	0.000	0.000	0.001
logicleTransform	0.640	0.012	0.652
logicletGml2-class	0.047	0.000	0.047
logtGml2-class	0.046	0.000	0.046
manyFilterResult-class	0.000	0.000	0.001
multipleFilterResult-class	0.001	0.000	0.001
norm2Filter-class	0.123	0.000	0.123
normalizeActionItem-class	0.001	0.000	0.001
normalizeView-class	0.000	0.000	0.001
parameters-methods	0.021	0.000	0.021
polygonGate	0.044	0.004	0.048
quadGate	0.154	0.004	0.158
quadratic-class	0.032	0.000	0.032
quadraticTransform	0.041	0.000	0.041
ratio-class	0.035	0.000	0.035
ratiotGml2-class	0.068	0.004	0.072
read.FCS	0.064	0.000	0.064
read.FCSheader	0.007	0.000	0.007
read.flowSet	0.113	0.000	0.113
rectangleGate	0.102	0.000	0.102
sampleFilter-class	0.036	0.000	0.036
scaleTransform	0.027	0.000	0.027
singleParameterTransform-class	0.001	0.000	0.001
sinht-class	0.024	0.000	0.024
split-methods	0.850	0.016	0.867
splitScaleTransform	1.263	0.004	1.266
splitscale-class	0.034	0.000	0.034
squareroot-class	0.028	0.000	0.029
subsettingActionItem-class	0.001	0.000	0.000
subsettingView-class	0.001	0.000	0.001
timeFilter-class	1.448	0.020	1.468
transform-class	0.002	0.000	0.003
transformActionItem-class	0.001	0.000	0.001
transformFilter-class	0.135	0.000	0.135
transformList-class	0.486	0.000	0.486
transformMap-class	0	0	0
transformView-class	0.001	0.000	0.001
truncateTransform	0.026	0.000	0.026
unitytransform-class	0.019	0.000	0.019
view-class	0.001	0.000	0.001
workFlow-class	0.002	0.000	0.001
write.FCS	0.048	0.000	0.048
write.flowSet	0.668	0.012	0.680

BioC 3.3: CHECK report for flowCore on linux2.bioconductor.org

Summary

Command output